X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=f9e8fdba4db2f673da6c0c458a6c8a912d758d55;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=88d9f24ddb63f7b3bdd113b4682465772e574128;hpb=04b756e96e1bfdfdb823b9857240837914135536;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 88d9f24..f9e8fdb 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.structure;
 
@@ -23,23 +22,44 @@ import java.util.*;
 
 import MCview.*;
 import jalview.analysis.*;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.StructureSelectionManagerProvider;
 import jalview.datamodel.*;
 
 public class StructureSelectionManager
 {
-  static StructureSelectionManager instance;
+  static IdentityHashMap<StructureSelectionManagerProvider,StructureSelectionManager> instances;
 
   StructureMapping[] mappings;
 
+  /**
+   * debug function - write all mappings to stdout
+   */
+  public void reportMapping() {
+    if (mappings==null)
+    {
+      System.err.println("reportMapping: No PDB/Sequence mappings.");
+    }else{
+      System.err.println("reportMapping: There are "+mappings.length+" mappings.");
+      for (int m=0;m<mappings.length;m++)
+      {
+        System.err.println("mapping "+m+" : "+mappings[m].pdbfile);
+      }
+    }
+  }
   Hashtable mappingData = new Hashtable();
 
-  public static StructureSelectionManager getStructureSelectionManager()
+  public static StructureSelectionManager getStructureSelectionManager(StructureSelectionManagerProvider context)
   {
-    if (instance == null)
+    if (instances == null)
     {
-      instance = new StructureSelectionManager();
+      instances = new java.util.IdentityHashMap<StructureSelectionManagerProvider,StructureSelectionManager>();
+    }
+    StructureSelectionManager instance=instances.get(context);
+    if (instance==null)
+    {
+      instances.put(context, instance=new StructureSelectionManager());
     }
-
     return instance;
   }
 
@@ -74,6 +94,10 @@ public class StructureSelectionManager
 
   Vector listeners = new Vector();
 
+  /**
+   * register a listener for alignment sequence mouseover events
+   * @param svl
+   */
   public void addStructureViewerListener(Object svl)
   {
     if (!listeners.contains(svl))
@@ -97,13 +121,28 @@ public class StructureSelectionManager
     return null;
   }
 
-  /*
-   * There will be better ways of doing this in the future, for now we'll use
-   * the tried and tested MCview pdb mapping
+  /**
+   * create sequence structure mappings between each sequence and the given
+   * pdbFile (retrieved via the given protocol).
+   * 
+   * @param sequence
+   *          - one or more sequences to be mapped to pdbFile
+   * @param targetChains
+   *          - optional chain specification for mapping each sequence to pdb
+   *          (may be nill, individual elements may be nill)
+   * @param pdbFile
+   *          - structure data resource
+   * @param protocol
+   *          - how to resolve data from resource
+   * @return null or the structure data parsed as a pdb file
    */
   synchronized public MCview.PDBfile setMapping(SequenceI[] sequence,
           String[] targetChains, String pdbFile, String protocol)
   {
+    /*
+     * There will be better ways of doing this in the future, for now we'll use
+     * the tried and tested MCview pdb mapping
+     */
     MCview.PDBfile pdb = null;
     try
     {
@@ -113,16 +152,32 @@ public class StructureSelectionManager
       ex.printStackTrace();
       return null;
     }
-
+    
     String targetChain;
     for (int s = 0; s < sequence.length; s++)
     {
+      boolean infChain = true;
       if (targetChains != null && targetChains[s] != null)
+      {
+        infChain = false;
         targetChain = targetChains[s];
+      }
       else if (sequence[s].getName().indexOf("|") > -1)
       {
         targetChain = sequence[s].getName().substring(
                 sequence[s].getName().lastIndexOf("|") + 1);
+        if (targetChain.length() > 1)
+        {
+          if (targetChain.trim().length() == 0)
+          {
+            targetChain = " ";
+          }
+          else
+          {
+            // not a valid chain identifier
+            targetChain = "";
+          }
+        }
       }
       else
         targetChain = "";
@@ -131,25 +186,37 @@ public class StructureSelectionManager
       AlignSeq maxAlignseq = null;
       String maxChainId = " ";
       PDBChain maxChain = null;
-
+      boolean first = true;
       for (int i = 0; i < pdb.chains.size(); i++)
       {
-        AlignSeq as = new AlignSeq(sequence[s], ((PDBChain) pdb.chains
-                .elementAt(i)).sequence, AlignSeq.PEP);
+        PDBChain chain = ((PDBChain) pdb.chains.elementAt(i));
+        if (targetChain.length() > 0 && !targetChain.equals(chain.id) && !infChain)
+        {
+          continue; // don't try to map chains don't match.
+        }
+        // TODO: correctly determine sequence type for mixed na/peptide
+        // structures
+        AlignSeq as = new AlignSeq(sequence[s],
+                ((PDBChain) pdb.chains.elementAt(i)).sequence,
+                ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA
+                        : AlignSeq.PEP);
         as.calcScoreMatrix();
         as.traceAlignment();
-        PDBChain chain = ((PDBChain) pdb.chains.elementAt(i));
 
-        if (as.maxscore > max
+        if (first || as.maxscore > max
                 || (as.maxscore == max && chain.id.equals(targetChain)))
         {
+          first = false;
           maxChain = chain;
           max = as.maxscore;
           maxAlignseq = as;
           maxChainId = chain.id;
         }
       }
-
+      if (maxChain == null)
+      {
+        continue;
+      }
       final StringBuffer mappingDetails = new StringBuffer();
       mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
               + maxChain.sequence.getSequenceAsString());
@@ -180,7 +247,9 @@ public class StructureSelectionManager
 
       maxChain.transferRESNUMFeatures(sequence[s], null);
 
-      int[][] mapping = new int[sequence[s].getEnd() + 2][2];
+      // allocate enough slots to store the mapping from positions in
+      // sequence[s] to the associated chain
+      int[][] mapping = new int[sequence[s].findPosition(sequence[s].getLength()) + 2][2];
       int resNum = -10000;
       int index = 0;
 
@@ -212,8 +281,8 @@ public class StructureSelectionManager
         pdbFile = "INLINE" + pdb.id;
 
       mappings[mappings.length - 1] = new StructureMapping(sequence[s],
-              pdbFile, pdb.id, maxChainId, mapping, mappingDetails
-                      .toString());
+              pdbFile, pdb.id, maxChainId, mapping,
+              mappingDetails.toString());
       maxChain.transferResidueAnnotation(mappings[mappings.length - 1]);
     }
     // ///////
@@ -221,32 +290,53 @@ public class StructureSelectionManager
     return pdb;
   }
 
-  public void removeStructureViewerListener(Object svl, String pdbfile)
+  public void removeStructureViewerListener(Object svl, String[] pdbfiles)
   {
     listeners.removeElement(svl);
-
+    if (svl instanceof SequenceListener)
+    {
+      for (int i=0;i<listeners.size();i++)
+      {
+        if (listeners.elementAt(i) instanceof StructureListener)
+        {
+          ((StructureListener)listeners.elementAt(i)).releaseReferences(svl);
+        }
+      }
+    }
+      
+    if (pdbfiles == null)
+    {
+      return;
+    }
     boolean removeMapping = true;
-
+    String[] handlepdbs;
+    Vector pdbs = new Vector();
+    for (int i = 0; i < pdbfiles.length; pdbs.addElement(pdbfiles[i++]))
+      ;
     StructureListener sl;
     for (int i = 0; i < listeners.size(); i++)
     {
       if (listeners.elementAt(i) instanceof StructureListener)
       {
         sl = (StructureListener) listeners.elementAt(i);
-        if (sl.getPdbFile().equals(pdbfile))
+        handlepdbs = sl.getPdbFile();
+        for (int j = 0; j < handlepdbs.length; j++)
         {
-          removeMapping = false;
-          break;
+          if (pdbs.contains(handlepdbs[j]))
+          {
+            pdbs.removeElement(handlepdbs[j]);
+          }
         }
+
       }
     }
 
-    if (removeMapping && mappings != null)
+    if (pdbs.size() > 0 && mappings != null)
     {
       Vector tmp = new Vector();
       for (int i = 0; i < mappings.length; i++)
       {
-        if (!mappings[i].pdbfile.equals(pdbfile))
+        if (!pdbs.contains(mappings[i].pdbfile))
         {
           tmp.addElement(mappings[i]);
         }
@@ -259,8 +349,15 @@ public class StructureSelectionManager
 
   public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
   {
+    if (listeners==null)
+    {
+      // old or prematurely sent event
+      return;
+    }
     boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
     SearchResults results = null;
+    SequenceI lastseq = null;
+    int lastipos = -1, indexpos;
     for (int i = 0; i < listeners.size(); i++)
     {
       if (listeners.elementAt(i) instanceof SequenceListener)
@@ -269,31 +366,39 @@ public class StructureSelectionManager
         {
           results = new SearchResults();
         }
-        int indexpos;
-        for (int j = 0; j < mappings.length; j++)
+        if (mappings != null)
         {
-          if (mappings[j].pdbfile.equals(pdbfile)
-                  && mappings[j].pdbchain.equals(chain))
+          for (int j = 0; j < mappings.length; j++)
           {
-            indexpos = mappings[j].getSeqPos(pdbResNum);
-            results.addResult(mappings[j].sequence, indexpos, indexpos);
-            // construct highlighted sequence list
-            if (seqmappings != null)
+            if (mappings[j].pdbfile.equals(pdbfile)
+                    && mappings[j].pdbchain.equals(chain))
             {
+              indexpos = mappings[j].getSeqPos(pdbResNum);
+              if (lastipos != indexpos && lastseq != mappings[j].sequence)
+              {
+                results.addResult(mappings[j].sequence, indexpos, indexpos);
+                lastipos = indexpos;
+                lastseq = mappings[j].sequence;
+                // construct highlighted sequence list
+                if (seqmappings != null)
+                {
 
-              Enumeration e = seqmappings.elements();
-              while (e.hasMoreElements())
+                  Enumeration e = seqmappings.elements();
+                  while (e.hasMoreElements())
 
-              {
-                ((AlignedCodonFrame) e.nextElement()).markMappedRegion(
-                        mappings[j].sequence, indexpos, results);
+                  {
+                    ((AlignedCodonFrame) e.nextElement()).markMappedRegion(
+                            mappings[j].sequence, indexpos, results);
+                  }
+                }
               }
+
             }
           }
         }
       }
     }
-    if (results.getSize() > 0)
+    if (results!=null)
     {
       for (int i = 0; i < listeners.size(); i++)
       {
@@ -310,15 +415,15 @@ public class StructureSelectionManager
    * highlight regions associated with a position (indexpos) in seq
    * 
    * @param seq
-   *                the sequeence that the mouse over occured on
+   *          the sequeence that the mouse over occured on
    * @param indexpos
-   *                the absolute position being mouseovered in seq (0 to
-   *                seq.length())
+   *          the absolute position being mouseovered in seq (0 to seq.length())
    * @param index
-   *                the sequence position (if -1, seq.findPosition is called to
-   *                resolve the residue number)
+   *          the sequence position (if -1, seq.findPosition is called to
+   *          resolve the residue number)
    */
-  public void mouseOverSequence(SequenceI seq, int indexpos, int index)
+  public void mouseOverSequence(SequenceI seq, int indexpos, int index,
+          VamsasSource source)
   {
     boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
     SearchResults results = null;
@@ -331,7 +436,10 @@ public class StructureSelectionManager
       if (listeners.elementAt(i) instanceof StructureListener)
       {
         sl = (StructureListener) listeners.elementAt(i);
-
+        if (mappings == null)
+        {
+          continue;
+        }
         for (int j = 0; j < mappings.length; j++)
         {
           if (mappings[j].sequence == seq
@@ -398,8 +506,8 @@ public class StructureSelectionManager
           // index);
           // pass the mouse over and absolute position onto the
           // VamsasListener(s)
-          ((VamsasListener) listeners.elementAt(i))
-                  .mouseOver(seq, indexpos);
+          ((VamsasListener) listeners.elementAt(i)).mouseOver(seq,
+                  indexpos, source);
         }
       }
     }
@@ -418,16 +526,17 @@ public class StructureSelectionManager
    * 
    * @param sequenceI
    * @param position
-   *                in an alignment sequence
+   *          in an alignment sequence
    */
-  public void mouseOverVamsasSequence(SequenceI sequenceI, int position)
+  public void mouseOverVamsasSequence(SequenceI sequenceI, int position,
+          VamsasSource source)
   {
     handlingVamsasMo = true;
     long msg = sequenceI.hashCode() * (1 + position);
     if (lastmsg != msg)
     {
       lastmsg = msg;
-      mouseOverSequence(sequenceI, position, -1);
+      mouseOverSequence(sequenceI, position, -1, source);
     }
     handlingVamsasMo = false;
   }
@@ -447,9 +556,10 @@ public class StructureSelectionManager
      * 
      * for (int j = 0; j < mappings.length; j++) {
      * 
-     * if (mappings[j].sequence == seq && mappings[j].getPdbId().equals(pdbid) &&
-     * mappings[j].pdbfile.equals(sl.getPdbFile())) { System.out.println(pdbid+"
-     * "+mappings[j].getPdbId() +" "+mappings[j].pdbfile);
+     * if (mappings[j].sequence == seq && mappings[j].getPdbId().equals(pdbid)
+     * && mappings[j].pdbfile.equals(sl.getPdbFile())) {
+     * System.out.println(pdbid+" "+mappings[j].getPdbId() +"
+     * "+mappings[j].pdbfile);
      * 
      * java.awt.Color col; for(int index=0; index<seq.getLength(); index++) {
      * if(jalview.util.Comparison.isGap(seq.getCharAt(index))) continue;
@@ -490,14 +600,16 @@ public class StructureSelectionManager
   public StructureMapping[] getMapping(String pdbfile)
   {
     Vector tmp = new Vector();
-    for (int i = 0; i < mappings.length; i++)
+    if (mappings != null)
     {
-      if (mappings[i].pdbfile.equals(pdbfile))
+      for (int i = 0; i < mappings.length; i++)
       {
-        tmp.addElement(mappings[i]);
+        if (mappings[i].pdbfile.equals(pdbfile))
+        {
+          tmp.addElement(mappings[i]);
+        }
       }
     }
-
     StructureMapping[] ret = new StructureMapping[tmp.size()];
     for (int i = 0; i < tmp.size(); i++)
     {
@@ -587,7 +699,8 @@ public class StructureSelectionManager
     modifySeqMappingList(true, codonFrames);
   }
 
-  Vector sel_listeners = new Vector();
+  Vector<SelectionListener> sel_listeners = new Vector<SelectionListener>();
+
   public void addSelectionListener(SelectionListener selecter)
   {
     if (!sel_listeners.contains(selecter))
@@ -595,6 +708,7 @@ public class StructureSelectionManager
       sel_listeners.addElement(selecter);
     }
   }
+
   public void removeSelectionListener(SelectionListener toremove)
   {
     if (sel_listeners.contains(toremove))
@@ -602,18 +716,98 @@ public class StructureSelectionManager
       sel_listeners.removeElement(toremove);
     }
   }
-  public synchronized void sendSelection(jalview.datamodel.SequenceGroup selection, jalview.datamodel.ColumnSelection colsel, SelectionSource source)
+
+  public synchronized void sendSelection(
+          jalview.datamodel.SequenceGroup selection,
+          jalview.datamodel.ColumnSelection colsel, SelectionSource source)
   {
-    if (sel_listeners!=null && sel_listeners.size()>0)
+    if (sel_listeners != null && sel_listeners.size() > 0)
     {
       Enumeration listeners = sel_listeners.elements();
       while (listeners.hasMoreElements())
       {
-        SelectionListener slis = ((SelectionListener) listeners.nextElement());
-        if (slis!=source) { 
-          slis.selection(selection, colsel, source); 
-        };
+        SelectionListener slis = ((SelectionListener) listeners
+                .nextElement());
+        if (slis != source)
+        {
+          slis.selection(selection, colsel, source);
+        }
+        ;
       }
     }
   }
+  
+  Vector<AlignmentViewPanelListener> view_listeners=new Vector<AlignmentViewPanelListener>();
+  public synchronized void sendViewPosition(jalview.api.AlignmentViewPanel source, int startRes,
+          int endRes, int startSeq, int endSeq)
+  {
+
+    if (view_listeners != null && view_listeners.size() > 0)
+    {
+      Enumeration<AlignmentViewPanelListener> listeners = view_listeners.elements();
+      while (listeners.hasMoreElements())
+      {
+        AlignmentViewPanelListener slis = listeners
+                .nextElement();
+        if (slis != source)
+        {
+          slis.viewPosition(startRes, endRes, startSeq, endSeq, source);
+        }
+        ;
+      }
+    }
+  }
+  
+
+  public void finalize() throws Throwable {
+    if (listeners!=null) {
+      listeners.clear();
+      listeners=null;
+    }
+    if (mappingData!=null)
+    {
+      mappingData.clear();
+      mappingData=null;
+    }
+    if (sel_listeners!=null)
+    {
+      sel_listeners.clear();
+      sel_listeners=null;
+    }
+    if (view_listeners!=null)
+    {
+      view_listeners.clear();
+      view_listeners=null;
+    }
+    mappings=null;
+    seqmappingrefs=null;
+  }
+
+  /**
+   * release all references associated with this manager provider
+   * @param jalviewLite
+   */
+  public static void release(StructureSelectionManagerProvider jalviewLite)
+  {
+//    synchronized (instances)
+    {
+      if (instances == null)
+      {
+        return;
+      }
+      StructureSelectionManager mnger = (instances.get(jalviewLite));
+      if (mnger != null)
+      {
+        instances.remove(jalviewLite);
+        try
+        {
+          mnger.finalize();
+        } catch (Throwable x)
+        {
+        }
+        ;
+      }
+    }
+  }
+
 }